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- PDB-9rdc: Crystal structure of Phytophthora infestans effector AVRcap1b in ... -

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Basic information

Entry
Database: PDB / ID: 9rdc
TitleCrystal structure of Phytophthora infestans effector AVRcap1b in complex with the ENTH domain of Nicotiana benthamiana NbTOL9a protein
Components
  • RxLR effector protein PITG_16705
  • Target of myb protein 1
KeywordsPROTEIN BINDING / Plant pathology / vesicle trafficking / ESCRT / plant immunity
Function / homology: / Effector PexRD54, WY-domain / host cell cytoplasm / extracellular region / RxLR effector protein PITG_16705
Function and homology information
Biological speciesPhytophthora infestans (potato late blight agent)
Nicotiana benthamiana (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsContreras, M.P. / Madhuprakash, J. / Lawson, D.M. / Kamoun, S.
Funding support United Kingdom, European Union, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V002937/1 United Kingdom
European Research Council (ERC)743165European Union
CitationJournal: To be published
Title: An effector from the potato late blight pathogen bridges the TOL9a vesicle trafficking protein to an activated helper NLR to suppress immunity
Authors: Madhuprakash, J. / Yuen, E.L.H. / Toghani, A. / Harvey, M. / Pai, H. / Bentham, A. / De la Concepcion, J.C. / Banfield, M.J. / Lawson, D.M. / Stevenson, C.E.M. / Derevnina, L. / Bozkurt, T.O. ...Authors: Madhuprakash, J. / Yuen, E.L.H. / Toghani, A. / Harvey, M. / Pai, H. / Bentham, A. / De la Concepcion, J.C. / Banfield, M.J. / Lawson, D.M. / Stevenson, C.E.M. / Derevnina, L. / Bozkurt, T.O. / Kamoun, S. / Contreras, M.P.
History
DepositionJun 2, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RxLR effector protein PITG_16705
B: RxLR effector protein PITG_16705
C: Target of myb protein 1
D: Target of myb protein 1


Theoretical massNumber of molelcules
Total (without water)174,9124
Polymers174,9124
Non-polymers00
Water00
1
A: RxLR effector protein PITG_16705
C: Target of myb protein 1


Theoretical massNumber of molelcules
Total (without water)87,4562
Polymers87,4562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-12 kcal/mol
Surface area38980 Å2
2
B: RxLR effector protein PITG_16705
D: Target of myb protein 1


Theoretical massNumber of molelcules
Total (without water)87,4562
Polymers87,4562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-8 kcal/mol
Surface area39240 Å2
Unit cell
Length a, b, c (Å)85.874, 136.912, 195.574
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RxLR effector protein PITG_16705


Mass: 70519.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminally truncated to remove signal peptide and RXLR-DEER motif. The starting GLY-PRO is left over from a 3C protease cleavage site. The third residue, ALA, corresponds to number 62 of ...Details: N-terminally truncated to remove signal peptide and RXLR-DEER motif. The starting GLY-PRO is left over from a 3C protease cleavage site. The third residue, ALA, corresponds to number 62 of the full wild-type sequence.
Source: (gene. exp.) Phytophthora infestans (potato late blight agent)
Gene: PITG_16705 / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 strain / References: UniProt: D0NVF3
#2: Protein Target of myb protein 1


Mass: 16936.877 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The starting GLY-PRO is left over from a 3C protease cleavage site. The third residue, MET, corresponds to number 1 of the full wild-type sequence. There is currently no Uniprot accession for this sequence.
Source: (gene. exp.) Nicotiana benthamiana (plant) / Gene: A4A49_18419 / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 strain
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: NULL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 4.1→79.57 Å / Num. obs: 18772 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 1 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.031 / Rrim(I) all: 0.11 / Χ2: 0.8 / Net I/σ(I): 9.6 / Num. measured all: 242580
Reflection shellResolution: 4.1→4.49 Å / % possible obs: 100 % / Redundancy: 13.6 % / Rmerge(I) obs: 2.126 / Num. measured all: 59716 / Num. unique obs: 4401 / CC1/2: 0.518 / Rpim(I) all: 0.595 / Rrim(I) all: 2.208 / Χ2: 0.68 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimless0.7.4data scaling
DIALSdata reduction
PHASER2.8.3phasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.1→79.57 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.937 / SU B: 213.92 / SU ML: 1.161 / Cross valid method: THROUGHOUT / ESU R Free: 0.974 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28596 938 5 %RANDOM
Rwork0.24815 ---
obs0.25005 17765 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 274.406 Å2
Baniso -1Baniso -2Baniso -3
1--4 Å2-0 Å20 Å2
2---2.54 Å20 Å2
3---6.53 Å2
Refinement stepCycle: 1 / Resolution: 4.1→79.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11839 0 0 0 11839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01212111
X-RAY DIFFRACTIONr_bond_other_d0.0020.01611678
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.83416392
X-RAY DIFFRACTIONr_angle_other_deg0.6441.78126945
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.07151466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.278564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12102202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.21809
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214086
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022742
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it13.64720.3365876
X-RAY DIFFRACTIONr_mcbond_other13.64720.3375876
X-RAY DIFFRACTIONr_mcangle_it22.49936.577338
X-RAY DIFFRACTIONr_mcangle_other22.49836.5697339
X-RAY DIFFRACTIONr_scbond_it12.70721.1366235
X-RAY DIFFRACTIONr_scbond_other12.70621.1366236
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other21.96338.6399055
X-RAY DIFFRACTIONr_long_range_B_refined36.25362.1189279
X-RAY DIFFRACTIONr_long_range_B_other36.249362.1189280
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 4.1→4.207 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 69 -
Rwork0.419 1262 -
obs--99.63 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5595-0.42480.63311.2574-0.94121.06920.0401-0.3339-0.09520.1999-0.0220.01440.0496-0.0367-0.01810.59380.13370.05130.61890.17610.050716.5451-41.5971-59.1756
22.0448-0.7251-0.0251.39990.30990.6724-0.1984-0.49390.5870.01850.14750.1081-0.188-0.12450.05091.05970.3313-0.32940.7884-0.25850.3326-6.773516.6485-67.5329
36.4553-1.32-0.22544.5331-0.69993.19430.09860.2455-0.3204-0.46160.0033-0.0917-0.27490.7989-0.10190.4211-0.2010.030.2955-0.05040.02831.6263-6.6737-107.4932
46.94462.95961.00781.67430.01581.9323-0.59350.98410.0448-0.1880.4224-0.6281-0.33610.00590.17110.88410.23470.04231.3072-0.11161.215441.4689-15.3058-86.7535
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 999
2X-RAY DIFFRACTION2B0 - 999
3X-RAY DIFFRACTION3C0 - 999
4X-RAY DIFFRACTION4D0 - 999

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